Well, here's the thing about Hawkeye, and it's an easy out for the writers of just about any of the currently active Marvel projects:

Hawkeye killed a lot of SHIELD agents and nearly destroyed the Helicarrier.
Doesn't matter that he was under mind control at the time; that's like trying to plead innocence for committing a slew of heinous murders while you were stoned, drunk, and/or insane. In the view of the courts, he's still guilty as sin.

So a logical explanation would be that, even after playing hero at the Battle of New York, Hawkeye *would* have to stand trial for numerous murders committed in Stuttgart and on the Helicarrier. There'd be *some* leniency there, given the circumstances, and his "shot at redemption" as an Avenger would definitely be taken into consideration, but in the end, the court would have to find him guilty of at least some kind of lesser manslaughter charges.

Bottom line --- Hawkeye probably went to jail. He most definitely would've lost his "badge" and SHIELD security clearances, and SHIELD would surely consider him too much of a security risk to re-hire.

I wouldn't be surprised to see that, in AOU, the Avengers will either bail him out or flat-out jailbreak him to get him back onto the team.